I just thought. We have that stupid gas issue. So is this a mineral issue? Think about Peaks of Baekdu. Bottom main is better because workers spawn closer to minerals. In upper main workers go little bit slowly to mine. :b
That's irrelevant, but top/bottom minerals in general tend to mine badly for zerg. Drones are very picky, and often will take retardedly long not-straight paths, but much less in vertical mineral formations than in horizontal.
Yes of course there is a mineral issue. But because of the higher number of mineral patches (8/9 vs 1 geysir), it becomes by far more complex than the gas issue.
Not only the position of minerals in relation to the main building matters, but also the position of the minerals to each other. You have to consider wandering (the Anthrax Edge) and whatnot.
From my experience, it can also matter if you just move the whole bunch of resources/starting location up or down 1 tile (no idea why this could be, SC's pathing is kinda weird).
Because the whole thing is too complex, I suggest that you simply make some test runs to see if the bases mine at approximately the same speed (5% difference and less would be a good value I guess). You should both test the mining speed when you start up with 4 workers and slowly produce more, and when you simply put 20+ workers there and mine for a couple of minutes. For zerg, a 9-12 drone test would be nice, too.
Make sure to always split workers nicely and equally on both positions etc.
By the way, stuff like manner pylon and reaver holes should be considered as well.